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(v3.0.0.9036) Prepare for v3.0.1

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dr. M.S. (Matthijs) Berends
2025-09-19 12:23:59 +01:00
parent 13f2a864da
commit 33fb1849eb
4 changed files with 13 additions and 7 deletions
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4
DESCRIPTION
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@@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 3.0.0.9035 Version: 3.0.0.9036
Date: 2025-09-18 Date: 2025-09-19
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by

2
NEWS.md
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# AMR 3.0.0.9035 # AMR 3.0.0.9036
This is a bugfix release following the release of v3.0.0 in June 2025. This is a bugfix release following the release of v3.0.0 in June 2025.

10
R/plotting.R
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@@ -284,11 +284,15 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
self$mic_values_levels[1] <- paste0("<=", self$mic_values_levels[1]) self$mic_values_levels[1] <- paste0("<=", self$mic_values_levels[1])
self$mic_values_levels[length(self$mic_values_levels)] <- paste0(">=", self$mic_values_levels[length(self$mic_values_levels)]) self$mic_values_levels[length(self$mic_values_levels)] <- paste0(">=", self$mic_values_levels[length(self$mic_values_levels)])
} }
self$mic_values_log <- log2(as.double(self$mic_values_rescaled)) self$mic_values_log <- log2(as.double(self$mic_values_rescaled))
if (aest == "y" && "group" %in% colnames(df) && "x" %in% colnames(df)) {
if (aest == "y" && "group" %in% colnames(df)) {
if (!"x" %in% colnames(df) || all(is.na(df$x))) {
out$group <- 1
} else {
out$group <- as.integer(factor(df$x)) out$group <- as.integer(factor(df$x))
} }
}
out[[aest]] <- self$mic_values_log out[[aest]] <- self$mic_values_log
} }
out out
@@ -329,7 +333,7 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
rng <- range(log2(as.mic(self$mic_values_levels))) rng <- range(log2(as.mic(self$mic_values_levels)))
# add 0.5 extra space # add 0.5 extra space
rng <- c(rng[1] - 0.5, rng[2] + 0.5) rng <- c(rng[1] - 0.5, rng[2] + 0.5)
if (!is.na(x[1]) && x[1] == 0) { if (!is.null(x) && !is.na(x[1]) && x[1] == 0) {
# scale that start at 0 must remain so, e.g. in case of geom_col() # scale that start at 0 must remain so, e.g. in case of geom_col()
rng[1] <- 0 rng[1] <- 0
} }

2
cran-comments.md
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This version is a bugfix release (v3.0.1) following the release of v3.0.0 in June 2025.
As with all previous >20 releases, some CHECKs on `oldrel` may return a `NOTE` for narrowly exceeding the installation size limit. This has been reduced to a minimum in prior coordination with CRAN maintainers and currently returns only an `INFO` on `release` and `devel`. As with all previous >20 releases, some CHECKs on `oldrel` may return a `NOTE` for narrowly exceeding the installation size limit. This has been reduced to a minimum in prior coordination with CRAN maintainers and currently returns only an `INFO` on `release` and `devel`.
We treat this as a high-impact package: it was published in the *Journal of Statistical Software* (2022), is listed in the CRAN Task View "Epidemiology", and (based on cranlogs download statistics) is used globally. If there is anything to address, we would appreciate being informed before archiving the current version. We conduct extensive automated unit testing and have no indication of unresolved issues. We treat this as a high-impact package: it was published in the *Journal of Statistical Software* (2022), is listed in the CRAN Task View "Epidemiology", and (based on cranlogs download statistics) is used globally. If there is anything to address, we would appreciate being informed before archiving the current version. We conduct extensive automated unit testing and have no indication of unresolved issues.